<div class="gmail_quote"><div class="HOEnZb"><div class="h5"><div class="gmail_quote"><br>Thank you Bradley, These images are blue channel of H&E stained images and you can see color images in mail attachment. I tried confidenceconnectedImageFilter on blue and VectorConfidenceConnectedImageFilter on RGB image. But most of time it crash when i give different values of InitialNeighborhoodRadius and Multiplier the nuclei. For Blue channel, it work
InitialNeighborhoodRadius = 1 and Multiplier = 2 and for color (RGB) it work on
InitialNeighborhoodRadius = 2 and Multiplier = 3. There results are not satisfactory, some time hole inside and some time oversegment. I also tried geodesic dilation, it doesn't effect the output.<div><br></div><div>
I am not getting suggestion regarding perceptual based color space. Do you mean HSV color space? </div><div><div><br></div><div>Can you suggest me some filters based Active Contour and level set based segmentation in ITK?</div>
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<div><br><div class="gmail_quote">On Thu, May 3, 2012 at 9:07 PM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello,<div><br></div><div>The images you provided are black and white shouldn't H&E stained image be color? You may tried using VectorConfidenceConnetedImageFilter, on the color image either with a single seed or in groups to estimate the global color range of the nuclei. You should also consider the color space used, and if it would be best to do the range in a perceptual based space, or not.</div>
<div><br></div><div>If the segmentation is predictable under-segmented by a certain number pixels around the boarder you may consider just refining the segmentation with a geodesic dilation of an over-segmentation.</div>
<div>
<br></div><div>Just a couple of suggestions to help you explore algorithms to try to find a solution to your problem.</div><div><br></div><div>Brad</div><div><br><div><div><div><div>On May 3, 2012, at 5:46 AM, Humayun Irshad wrote:</div>
<br></div></div><blockquote type="cite"><div><div>ITK Experts,<div><br></div><div>I need to segment nuclei (specially mitosis nuclei) in H&E stained histopathological images (see in attachment). I have seed points. I tried ConfidenceConnectedImageFilter and FastMarchingImageFilter but it give poor results. Most of the time, nuclei are under segment. Mitosis nuclei are homogeneous and having variations in shape and size. Please suggest any better segmentation filter. </div>
<div><br></div>-- <br><font face="arial, helvetica, sans-serif">-- <br>Best Regards, <br><br></font><div><b><font face="arial, helvetica, sans-serif">HUMAYUN IRSHAD</font></b></div><div><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div>
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<font face="Helvetica" size="3" style="font:normal normal normal 12px/normal Helvetica">========================================================</font></p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
<font face="Helvetica" size="3" style="font:normal normal normal 12px/normal Helvetica">Bradley Lowekamp<span> </span><span> </span></font></p><p style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
<font face="Helvetica" size="3" style="font:normal normal normal 12px/normal Helvetica">Medical Science and Computing for</font></p>
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<font face="Helvetica" size="3" style="font:normal normal normal 12px/normal Helvetica"><a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a></font></p><br></span></div></span></span><br>
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<br></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><font face="arial, helvetica, sans-serif">-- <br>Best Regards, <br><br></font><div><b><font face="arial, helvetica, sans-serif">HUMAYUN IRSHAD</font></b></div>
<div><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div style="display:inline!important">
<span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">PhD student, University of Joseph Fourier, Grenoble, France</font></span></b></span></div>
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<span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">IPAL – Image & Pervasive Access Lab, Singapore</font></span></b></span></div>
</span></b></span><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">UMI CNRS (I2R/A*STAR, NUS, UJF, UPMC, IT)</font></span></b></span></div>
<div><div><div><span style="border-collapse:collapse"><font face="arial, helvetica, sans-serif"><div><span style="border-collapse:collapse"><br></span></div>Institute for Infocomm Research (I2R)<br>1 Fusionopolis Way<br>
#10-19 Connexis South Tower<br>
Singapore 138632<br>Tel:<a href="tel:%2B65-65162864" value="+6565162864" target="_blank">+65-65162864</a></font></span></div></div></div><div><span style="border-collapse:collapse"><font face="arial, helvetica, sans-serif">Cell: <a href="tel:%2B65-83851671" value="+6583851671" target="_blank">+65-83851671</a></font></span></div>
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</div></div></div><br><br clear="all"><div><br></div>-- <br><font face="arial, helvetica, sans-serif">-- <br>Best Regards, <br><br></font><div><b><font face="arial, helvetica, sans-serif">HUMAYUN IRSHAD</font></b></div><div>
<span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div style="display:inline!important">
<span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">PhD student, University of Joseph Fourier, Grenoble, France</font></span></b></span></div>
</span></b></span></div></span></b></span><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div style="display:inline!important"><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div style="display:inline!important">
<span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">Research Engineer, </font></span></b></span></div></span></b></span></div></span></b></span><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div style="display:inline!important">
<span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">IPAL – Image & Pervasive Access Lab, Singapore</font></span></b></span></div>
</span></b></span><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><div><span style="border-collapse:collapse"><b><span style="border-collapse:separate;font-weight:normal"><font face="arial, helvetica, sans-serif">UMI CNRS (I2R/A*STAR, NUS, UJF, UPMC, IT)</font></span></b></span></div>
<div><div><div><span style="border-collapse:collapse"><font face="arial, helvetica, sans-serif"><div><span style="border-collapse:collapse"><br></span></div>Institute for Infocomm Research (I2R)<br>1 Fusionopolis Way<br>#10-19 Connexis South Tower<br>
Singapore 138632<br>Tel:+65-65162864</font></span></div></div></div><div><span style="border-collapse:collapse"><font face="arial, helvetica, sans-serif">Cell: +65-83851671</font></span></div><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><br>
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